Most state-of-the-art Graph Neural Networks (GNNs) can be defined as a form of graph convolution which can be realized by message passing between direct neighbors or beyond. To scale such GNNs to large graphs, various neighbor-, layer-, or subgraph-sampling techniques are proposed to alleviate the "neighbor explosion" problem by considering only a small subset of messages passed to the nodes in a mini-batch. However, sampling-based methods are difficult to apply to GNNs that utilize many-hops-away or global context each layer, show unstable performance for different tasks and datasets, and do not speed up model inference. We propose a principled and fundamentally different approach, VQ-GNN, a universal framework to scale up any convolution-based GNNs using Vector Quantization (VQ) without compromising the performance. In contrast to sampling-based techniques, our approach can effectively preserve all the messages passed to a mini-batch of nodes by learning and updating a small number of quantized reference vectors of global node representations, using VQ within each GNN layer. Our framework avoids the "neighbor explosion" problem of GNNs using quantized representations combined with a low-rank version of the graph convolution matrix. We show that such a compact low-rank version of the gigantic convolution matrix is sufficient both theoretically and experimentally. In company with VQ, we design a novel approximated message passing algorithm and a nontrivial back-propagation rule for our framework. Experiments on various types of GNN backbones demonstrate the scalability and competitive performance of our framework on large-graph node classification and link prediction benchmarks.
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Learning to Simulate Complex Physics with Graph Networks
Here we present a machine learning framework and model implementation that can learn to simulate a wide variety of challenging physical domains, involving fluids, rigid solids, and deformable materials interacting with one another. Our framework—which we term “Graph Network-based Simulators” (GNS)—represents the state of a physical system with particles, expressed as nodes in a graph, and computes dynamics via learned message-passing. Our results show that our model can generalize from single-timestep predictions with thousands of particles during training, to different initial conditions, thousands of timesteps, and at least an order of magnitude more particles at test time. Our model was robust to hyperparameter choices across various evaluation metrics: the main determinants of long-term performance were the number of message-passing steps, and mitigating the accumulation of error by corrupting the training data with noise. Our GNS framework advances the state-of-the-art in learned physical simulation, and holds promise for solving a wide range of complex forward and inverse problems.
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- Award ID(s):
- 1835598
- NSF-PAR ID:
- 10198856
- Date Published:
- Journal Name:
- International Conference on Machine Learning (ICML)
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Graphs/Networks are common in real-world applications where data have rich content and complex relationships. The increasing popularity also motivates many network learning algorithms, such as community detection, clustering, classification, and embedding learning, etc.. In reality, the large network volumes often hider a direct use of learning algorithms to the graphs. As a result, it is desirable to have the flexibility to condense a network to an arbitrary size, with well-preserved network topology and node content information. In this paper, we propose a graph compression network (GEN) to achieve network compression and embedding at the same time. Our theme is to leverage the network topology to find node mappings, such that densely connected nodes, including their node content, are compressed as a new node, with a latent vector (i.e. embedding) being learned to represent the compressed node. In addition to compression learning, we also develop a novel encoding-decoding framework, using feature diffusion process, to "decompress" the condensed network. Different from traditional graph convolution which uses direct-neighbor message passing, our decompression advocates high-order message passing within compressed nodes to learning feature representation for all nodes in the network. A unique strength of GEN is that it leverages the graph neural network principle to learn mapping automatically, so one can compress a network to an arbitrary size, and also decompress it to the original node space with minimum information loss. Experiments and comparisons confirm that GEN can automatically find clusters and communities, and compress them as new nodes. Results also show that GEN achieves improved performance for numerous tasks, including graph classification and node clustering.more » « less
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Simulating the dynamics of ions near polarizable nanoparticles (NPs) using coarse-grained models is extremely challenging due to the need to solve the Poisson equation at every simulation timestep. Recently, a molecular dynamics (MD) method based on a dynamical optimization framework bypassed this obstacle by representing the polarization charge density as virtual dynamic variables and evolving them in parallel with the physical dynamics of ions. We highlight the computational gains accessible with the integration of machine learning (ML) methods for parameter prediction in MD simulations by demonstrating how they were realized in MD simulations of ions near polarizable NPs. An artificial neural network–based regression model was integrated with MD simulation and predicted the optimal simulation timestep and optimization parameters characterizing the virtual system with 94.3% success. The ML-enabled auto-tuning of parameters generated accurate dynamics of ions for ≈ 10 million steps while improving the stability of the simulation by over an order of magnitude. The integration of ML-enhanced framework with hybrid Open Multi-Processing / Message Passing Interface (OpenMP/MPI) parallelization techniques reduced the computational time of simulating systems with thousands of ions and induced charges from thousands of hours to tens of hours, yielding a maximum speedup of ≈ 3 from ML-only acceleration and a maximum speedup of ≈ 600 from the combination of ML and parallel computing methods. Extraction of ionic structure in concentrated electrolytes near oil–water emulsions demonstrates the success of the method. The approach can be generalized to select optimal parameters in other MD applications and energy minimization problems.more » « less
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There has been significant progress in improving the performance of graph neural networks (GNNs) through enhancements in graph data, model architecture design, and training strategies. For fairness in graphs, recent studies achieve fair representations and predictions through either graph data pre-processing (e.g., node feature masking, and topology rewiring) or fair training strategies (e.g., regularization, adversarial debiasing, and fair contrastive learning). How to achieve fairness in graphs from the model architecture perspective is less explored. More importantly, GNNs exhibit worse fairness performance compared to multilayer perception since their model architecture (i.e., neighbor aggregation) amplifies biases. To this end, we aim to achieve fairness via a new GNN architecture. We propose Fair Message Passing (FMP) designed within a unified optimization framework for GNNs. Notably, FMP explicitly renders sensitive attribute usage in forward propagation for node classification task using cross-entropy loss without data pre-processing. In FMP, the aggregation is first adopted to utilize neighbors' information and then the bias mitigation step explicitly pushes demographic group node presentation centers together.In this way, FMP scheme can aggregate useful information from neighbors and mitigate bias to achieve better fairness and prediction tradeoff performance. Experiments on node classification tasks demonstrate that the proposed FMP outperforms several baselines in terms of fairness and accuracy on three real-world datasets. The code is available at https://github.com/zhimengj0326/FMP.
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Accepted Manuscript1.0
- Conference Paper:
- The DOI is not currently available.
